OpenSim Extensible software for modeling, simulating, controlling, and analyzing the neuromusculoskeletal system. Scott Delp, Clay Anderson Ayman Habib Neuromuscular Simulation Package Toolkit https://simtk.org/home/opensim Development with public userbase MIT license Application Simbios Center 0.8 4/7/07 OpenSim Extensible software for modeling, simulating, controlling, and analyzing the neuromusculoskeletal system. Scott Delp, Clay Anderson Ayman Habib Neuromuscular Simulation Package Mechanical Simulation https://simtk.org/home/opensim Development with public userbase MIT license Application Simbios Center 0.8 4/7/07 SimVascular Open source release of tools for cardiovascular simulation Taylor Group Cardiovascular Toolkit Simulation https://simtk.org/home/simvascular Development with public userbase Multiple licenses Application Simbios Center Simbody SimTK core toolset providing general multibody dynamics capability Michael Sherman SimTK Core component, multibody Dynamics MultibodyDynamics https://simtk.org/home/simbody Development MIT license Class Library / Toolkit Simbios Center ToRNADO Application for animating and visualising RNA Christopher Bruns RNA vizualisation Molecular Structure Viewers https://simtk.org/home/rna-viz-proto Mature MIT license Application Simbios Center 1 1/30/07 ISIM Graphical user interface for ISIM, is package that simulates the thermodynamic ensemble of ions around a macromolecule. Christopher Bruns, Mark Engelhardt, Mark Friedrichs Ionic environment of proteins Simulation https://simtk.org/home/isim_interface Mature Multiple licenses Application Simbios Center 1.3 5/8/07 Lapack High quality, high performance numerical methods for matrix arithmetic and for solving linear algebra problems Jack Middleton LAPACK linear algebra library (with BLAS) Toolkit https://simtk.org/home/lapack Mature MIT license Class Library / Toolkit Simbios Center Lapack High quality, high performance numerical methods for matrix arithmetic and for solving linear algebra problems Jack Middleton LAPACK linear algebra library (with BLAS) LinearAlgebraTools https://simtk.org/home/lapack Mature MIT license Class Library / Toolkit Simbios Center BioSimulation Course Biosimulation Course using the SimTK toolkit Paul Mitiguy, Russ Altman, Scott, Delp, Magda Jonikas, Chand John Biosimulation Course Course Material https://simtk.org/home/training Development with public userbase MIT license Documents Simbios Center 4/15/07 Allopathfinder An easy to use application to find allosteric communication pathway in proteins Susan Tang, Jung-Chi Liao, Alex Dunn, Russ Altman, James Spudich, Jeanette Schmidt Myosin Allosteric Communication Structure-based protein classification https://simtk.org/home/allopathfinder Development with public userbase MIT license Application Simbios Center 1.1 4/15/07 Cardiovascular Model Repository Geometric models collected from research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford Peter Feenstra Cardiovascular, Models Clinical data https://simtk.org/home/cv-gmodels Mature MIT license Models Simbios Center 1 4/4/06 CPODES numerical integrator Numerical integrator for solving multibody dynamics problems Michael Sherman, Radu Serban Numerical integrator Numerical Methods https://simtk.org/home/cpodes Mature MIT license Class Library / Toolkit Simbios Center 1 4/7/07 SAFA Quantitative analysis of gels from hydroxyl radical footprinting and other structure mapping techniques Das, R., Laederach, A. Pearlman, S. M., Herschlag, D, & Altman, R.B Analysis of gels BasicResearch https://simtk.org/home/safa Mature MIT license Application Simbios Center 11 4/7/07 Discrete Center Hierarchies Data structure for the maintenance of proximity information of a set of moving points. J. Gao, L.J. Guibas, and A. Nguyen Data structure for the maintenance of proximity information Algorithm https://simtk.org/home/dch Mature MIT license Application Simbios Center 6/15/06 Feature Tools that produce representations of key biophysical and biochemical features that are critical for understanding function Altman Toolsproducing representations of key biophysical and biochemical features from structure data that are critical for understanding function Structure-based protein classification https://simtk.org/home/feature Mature MIT license Application Simbios Center